test.yaml

name: Test

on:
  push:
    branches: [main]
  pull_request:
    branches: [main]
  schedule:
    - cron: "0 5 1,15 * *"

concurrency:
  group: ${{ github.workflow }}-${{ github.ref }}
  cancel-in-progress: true

env:
  # TODO: Remove once hatch supports virtualenv>=21, see https://github.com/pypa/hatch/pull/2196
  UV_CONSTRAINT: .github/workflows/constraints.txt

jobs:
  # Get the test environment from hatch as defined in pyproject.toml.
  # This ensures that the pyproject.toml is the single point of truth for test definitions and the same tests are
  # run locally and on continuous integration.
  # Check [[tool.hatch.envs.hatch-test.matrix]] in pyproject.toml and https://hatch.pypa.io/latest/environment/ for
  # more details.
  get-environments:
    runs-on: ubuntu-latest
    outputs:
      envs: ${{ steps.get-envs.outputs.envs }}
    steps:
      - uses: actions/checkout@v5
        with:
          filter: blob:none
          fetch-depth: 0
      - name: Install uv
        uses: astral-sh/setup-uv@v7
      - name: Get test environments
        id: get-envs
        run: |
          ENVS_JSON=$(uvx hatch env show --json | jq -c 'to_entries
            | map(
                select(.key | startswith("hatch-test"))
                | {
                    name: .key,
                    label: (if (.key | contains("pre")) then .key + " (PRE-RELEASE DEPENDENCIES)" else .key end),
                    python: .value.python
                  }
              )')
          echo "envs=${ENVS_JSON}" | tee $GITHUB_OUTPUT

  # Run tests through hatch. Spawns a separate runner for each environment defined in the hatch matrix obtained above.
  test:
    needs: get-environments

    strategy:
      fail-fast: false
      matrix:
        os: [ubuntu-latest]
        env: ${{ fromJSON(needs.get-environments.outputs.envs) }}

    name: ${{ matrix.env.label }}
    runs-on: ${{ matrix.os }}

    steps:
      - uses: actions/checkout@v5
        with:
          filter: blob:none
          fetch-depth: 0
      - name: Setup R
        uses: r-lib/actions/setup-r@v2
        with:
          r-version: 'release'
          use-public-rspm: true
      - name: Get R version for cache key
        id: r-version
        run: echo "version=$(R --version | head -n1 | cut -d' ' -f3)" >> $GITHUB_OUTPUT
      - name: Cache R packages
        id: cache-r-packages
        uses: actions/cache@v4
        with:
          path: ${{ env.R_LIBS_USER }}
          key: ${{ runner.os }}-r-${{ steps.r-version.outputs.version }}-${{ hashFiles('.github/workflows/test.yaml') }}
          restore-keys: |
            ${{ runner.os }}-r-${{ steps.r-version.outputs.version }}-
            ${{ runner.os }}-r-
      - name: Install R packages
        if: steps.cache-r-packages.outputs.cache-hit != 'true'
        run: |
          R -e 'if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")'
          R -e 'BiocManager::install(c("limma", "rhdf5"), update=FALSE, ask=FALSE)'
          R -e 'install.packages(c("Matrix", "magrittr", "data.table", "glue", "stringr"), repos="https://cloud.r-project.org")'
      - name: Install uv
        uses: astral-sh/setup-uv@v7
        with:
          python-version: ${{ matrix.env.python }}
      - name: create hatch environment
        run: uvx hatch env create ${{ matrix.env.name }}
      - name: run tests using hatch
        env:
          MPLBACKEND: agg
          PLATFORM: ${{ matrix.os }}
          DISPLAY: :42
        run: uvx hatch run ${{ matrix.env.name }}:run-cov -v --color=yes -n auto
      - name: generate coverage report
        run: |
          # See https://coverage.readthedocs.io/en/latest/config.html#run-patch
          test -f .coverage || uvx hatch run ${{ matrix.env.name }}:cov-combine
          uvx hatch run ${{ matrix.env.name }}:cov-report   # report visibly
          uvx hatch run ${{ matrix.env.name }}:coverage xml # create report for upload
      - name: Upload coverage
        uses: codecov/codecov-action@v5

  # Check that all tests defined above pass. This makes it easy to set a single "required" test in branch
  # protection instead of having to update it frequently. See https://github.com/re-actors/alls-green#why.
  check:
    name: Tests pass in all hatch environments
    if: always()
    needs:
      - get-environments
      - test
    runs-on: ubuntu-latest
    steps:
        - uses: re-actors/alls-green@release/v1
          with:
            jobs: ${{ toJSON(needs) }}